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Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan

Since its emergence in China, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide including Pakistan. During the pandemic, whole genome sequencing has played an important role in understanding the evolution and genomic diversity of SARS-CoV-2. Although an unprecedented...

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Autores principales: Umair, Massab, Ikram, Aamer, Salman, Muhammad, Khurshid, Adnan, Alam, Masroor, Badar, Nazish, Suleman, Rana, Tahir, Faheem, Sharif, Salmaan, Montgomery, Joel, Whitmer, Shannon, Klena, John
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7987156/
https://www.ncbi.nlm.nih.gov/pubmed/33755704
http://dx.doi.org/10.1371/journal.pone.0248371
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author Umair, Massab
Ikram, Aamer
Salman, Muhammad
Khurshid, Adnan
Alam, Masroor
Badar, Nazish
Suleman, Rana
Tahir, Faheem
Sharif, Salmaan
Montgomery, Joel
Whitmer, Shannon
Klena, John
author_facet Umair, Massab
Ikram, Aamer
Salman, Muhammad
Khurshid, Adnan
Alam, Masroor
Badar, Nazish
Suleman, Rana
Tahir, Faheem
Sharif, Salmaan
Montgomery, Joel
Whitmer, Shannon
Klena, John
author_sort Umair, Massab
collection PubMed
description Since its emergence in China, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide including Pakistan. During the pandemic, whole genome sequencing has played an important role in understanding the evolution and genomic diversity of SARS-CoV-2. Although an unprecedented number of SARS-CoV-2 full genomes have been submitted in GISAID and NCBI, data from Pakistan is scarce. We report the sequencing, genomic characterization, and phylogenetic analysis of five SARS-CoV-2 strains isolated from patients in Pakistan. The oropharyngeal swabs of patients that were confirmed positive for SARS-CoV-2 through real-time RT-PCR at National Institute of Health, Pakistan, were selected for whole-genome sequencing. Sequencing was performed using NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEW ENGLAND BioLabs Inc., MA, US) and Illumina iSeq 100 instrument (Illumina, San Diego, US). Based on whole-genome analysis, three Pakistani SARS-CoV-2 strains clustered into the 20A (GH) clade along with the strains from Oman, Slovakia, United States, and Pakistani strain EPI_ISL_513925. The two 19B (S)-clade strains were closely related to viruses from India and Oman. Overall, twenty-nine amino acid mutations were detected in the current study genome sequences, including fifteen missense and four novel mutations. Notably, we have found a D614G (aspartic acid to glycine) mutation in spike protein of the sequences from the GH clade. The G614 variant carrying the characteristic D614G mutation has been shown to be more infectious that lead to its rapid spread worldwide. This report highlights the detection of GH and S clade strains and G614 variant from Pakistan warranting large-scale whole-genome sequencing of strains prevalent in different regions to understand virus evolution and to explore their genetic diversity.
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spelling pubmed-79871562021-04-02 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan Umair, Massab Ikram, Aamer Salman, Muhammad Khurshid, Adnan Alam, Masroor Badar, Nazish Suleman, Rana Tahir, Faheem Sharif, Salmaan Montgomery, Joel Whitmer, Shannon Klena, John PLoS One Research Article Since its emergence in China, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide including Pakistan. During the pandemic, whole genome sequencing has played an important role in understanding the evolution and genomic diversity of SARS-CoV-2. Although an unprecedented number of SARS-CoV-2 full genomes have been submitted in GISAID and NCBI, data from Pakistan is scarce. We report the sequencing, genomic characterization, and phylogenetic analysis of five SARS-CoV-2 strains isolated from patients in Pakistan. The oropharyngeal swabs of patients that were confirmed positive for SARS-CoV-2 through real-time RT-PCR at National Institute of Health, Pakistan, were selected for whole-genome sequencing. Sequencing was performed using NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEW ENGLAND BioLabs Inc., MA, US) and Illumina iSeq 100 instrument (Illumina, San Diego, US). Based on whole-genome analysis, three Pakistani SARS-CoV-2 strains clustered into the 20A (GH) clade along with the strains from Oman, Slovakia, United States, and Pakistani strain EPI_ISL_513925. The two 19B (S)-clade strains were closely related to viruses from India and Oman. Overall, twenty-nine amino acid mutations were detected in the current study genome sequences, including fifteen missense and four novel mutations. Notably, we have found a D614G (aspartic acid to glycine) mutation in spike protein of the sequences from the GH clade. The G614 variant carrying the characteristic D614G mutation has been shown to be more infectious that lead to its rapid spread worldwide. This report highlights the detection of GH and S clade strains and G614 variant from Pakistan warranting large-scale whole-genome sequencing of strains prevalent in different regions to understand virus evolution and to explore their genetic diversity. Public Library of Science 2021-03-23 /pmc/articles/PMC7987156/ /pubmed/33755704 http://dx.doi.org/10.1371/journal.pone.0248371 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication.
spellingShingle Research Article
Umair, Massab
Ikram, Aamer
Salman, Muhammad
Khurshid, Adnan
Alam, Masroor
Badar, Nazish
Suleman, Rana
Tahir, Faheem
Sharif, Salmaan
Montgomery, Joel
Whitmer, Shannon
Klena, John
Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan
title Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan
title_full Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan
title_fullStr Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan
title_full_unstemmed Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan
title_short Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan
title_sort whole-genome sequencing of sars-cov-2 reveals the detection of g614 variant in pakistan
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7987156/
https://www.ncbi.nlm.nih.gov/pubmed/33755704
http://dx.doi.org/10.1371/journal.pone.0248371
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